Locus 128

Sequence ID 2R_DroMel_CAF1
Location 1,389,267 – 1,389,395
Length 128
Max. P 0.711705
window268 window269 window270

overview

Window 8

Location 1,389,267 – 1,389,364
Length 97
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.63
Mean single sequence MFE -32.20
Consensus MFE -24.62
Energy contribution -26.46
Covariance contribution 1.84
Combinations/Pair 1.04
Mean z-score -1.45
Structure conservation index 0.76
SVM decision value 0.08
SVM RNA-class probability 0.573402
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1389267 97 + 20766785
UAACU-----------------GCGGCCCGAGCGACUUGCUGCUGACGGCAGCUUUGUGUCGAUGACGAUGCU------UUCAAAUGGGCGAAAGCUGAAUGGCAUUUUGGCCAUUUUCA
.....-----------------..((((....((((..(((((.....))))).....)))).....((((((------((((.....((....)))))).))))))..))))....... ( -32.00)
>DroSec_CAF1 16259 103 + 1
UAACU-----------------GAGGCCCAAGCGACUCGCUGCUGACGGCAGCUUUGUGUCGAUGACGAUGCUUUGCUUUUCAAAUGGGCGAAAGCUGAAUGGCAUUUUGUCCAUUUUCA
.....-----------------(((....((((((...(((((.....)))))...((((((....)))))).)))))))))(((((((((((((((....))).))))))))))))... ( -34.20)
>DroSim_CAF1 21007 103 + 1
UAACU-----------------GAGGCCCAAGCGACUUGCUGCUGACGGCAGCUUUGUGUCGAUGACGAUGCUUUGCUUUUCAAAUGGGCGAAAGCUGAAUGGCAUUUUGGCCAUUUUCA
.....-----------------...((((((((((...(((((.....)))))...((((((....)))))).))))).......))))).......(((((((......)))))))... ( -33.41)
>DroEre_CAF1 14432 82 + 1
--------------------------CCCAAGUGACUUGCUGCCGACGGCAGCUUUGUGCCGAU------GCU------UUCAAAUGGGCGAAAGCUGAAUGGCAUUUUGGCCAUUUUCA
--------------------------.(((..(((...((((((...)))))).....((....------)).------.)))..)))((....)).(((((((......)))))))... ( -27.30)
>DroYak_CAF1 12172 108 + 1
UAACUGUGCCCAAGCGUAGACUGAGGCCCAAGAGACUUGCUGCUGACGGCAGCUUUGUGCCGAU------GCU------UUCAAAUGGGCGAAAGCUGAAUGGCAUUUUGGCCAUUUUCA
...((((((....)))))).....((((.((((.....(((((.....)))))....(((((..------(((------(((........))))))....)))))))))))))....... ( -34.10)
>consensus
UAACU_________________GAGGCCCAAGCGACUUGCUGCUGACGGCAGCUUUGUGUCGAUGACGAUGCU______UUCAAAUGGGCGAAAGCUGAAUGGCAUUUUGGCCAUUUUCA
.........................(((((........(((((.....)))))...((((((....)))))).............))))).......(((((((......)))))))... (-24.62 = -26.46 +   1.84) 

alignment

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secondary structure

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dotplot

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Window 9

Location 1,389,267 – 1,389,364
Length 97
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.63
Mean single sequence MFE -28.44
Consensus MFE -19.56
Energy contribution -21.44
Covariance contribution 1.88
Combinations/Pair 1.04
Mean z-score -1.57
Structure conservation index 0.69
SVM decision value 0.06
SVM RNA-class probability 0.565981
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1389267 97 - 20766785
UGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAA------AGCAUCGUCAUCGACACAAAGCUGCCGUCAGCAGCAAGUCGCUCGGGCCGC-----------------AGUUA
(((..(((((......))))))))(((((((......))))------))).(((....))).....((((((.(((.(.(((.....)))).))).))-----------------)))). ( -29.50)
>DroSec_CAF1 16259 103 - 1
UGAAAAUGGACAAAAUGCCAUUCAGCUUUCGCCCAUUUGAAAAGCAAAGCAUCGUCAUCGACACAAAGCUGCCGUCAGCAGCGAGUCGCUUGGGCCUC-----------------AGUUA
....(((((.(.....)))))).((((...(((((..(((...((......(((....)))......((((....)))).))...)))..)))))...-----------------)))). ( -26.20)
>DroSim_CAF1 21007 103 - 1
UGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAAAAGCAAAGCAUCGUCAUCGACACAAAGCUGCCGUCAGCAGCAAGUCGCUUGGGCCUC-----------------AGUUA
....((((((......)))))).((((...(((((..(((...........(((....)))......(((((.....)))))...)))..)))))...-----------------)))). ( -28.80)
>DroEre_CAF1 14432 82 - 1
UGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAA------AGC------AUCGGCACAAAGCUGCCGUCGGCAGCAAGUCACUUGGG--------------------------
.........((((..((((.....(((((((......))))------)))------...))))....((((((...)))))).......)))).-------------------------- ( -25.80)
>DroYak_CAF1 12172 108 - 1
UGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAA------AGC------AUCGGCACAAAGCUGCCGUCAGCAGCAAGUCUCUUGGGCCUCAGUCUACGCUUGGGCACAGUUA
.......((((....((((.....(((((((......))))------)))------...))))....(((((.....)))))..........))))...(((((....)))))....... ( -31.90)
>consensus
UGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAA______AGCAUCGUCAUCGACACAAAGCUGCCGUCAGCAGCAAGUCGCUUGGGCCUC_________________AGUUA
(((..(((((......))))))))......(((((..(((...........(((....)))......(((((.....)))))...)))..)))))......................... (-19.56 = -21.44 +   1.88) 

alignment

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secondary structure

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dotplot

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Window 0

Location 1,389,290 – 1,389,395
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.78
Mean single sequence MFE -37.24
Consensus MFE -27.03
Energy contribution -27.58
Covariance contribution 0.55
Combinations/Pair 1.07
Mean z-score -1.80
Structure conservation index 0.73
SVM decision value 0.38
SVM RNA-class probability 0.711705
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1389290 105 - 20766785
GAGUCGUCAGCGUCG---------UCAGCGCCGUCGUGGGUGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAA------AGCAUCGUCAUCGACACAAAGCUGCCGUCAGCA
.........((..((---------.((((((..(((((((((((((((((......))))).....))))))))))..)).------.)).(((....)))......)))).))...)). ( -35.00)
>DroSec_CAF1 16282 111 - 1
GCGUCGUCAGCGUCG---------UCAGAGGCGUCGUGGGUGAAAAUGGACAAAAUGCCAUUCAGCUUUCGCCCAUUUGAAAAGCAAAGCAUCGUCAUCGACACAAAGCUGCCGUCAGCA
((..((.((((...(---------((.((((((..((((((((((((((.(.....))))).....)))))))).((((.....))))))..)))).))))).....)))).))...)). ( -34.60)
>DroSim_CAF1 21030 111 - 1
GCGUCGUCAGCGUCG---------UCAGCGGCGUCGUGGGUGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAAAAGCAAAGCAUCGUCAUCGACACAAAGCUGCCGUCAGCA
((..((.((((((((---------....))))((((((((((((((((((......))))).....)))))))))((((.....))))..........)))).....)))).))...)). ( -39.20)
>DroEre_CAF1 14446 108 - 1
GCGUCGUCAGCGUCGUCAGCGUCGUCAGCGCCGCCGUGGGUGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAA------AGC------AUCGGCACAAAGCUGCCGUCGGCA
(((.(((..(((.((....)).)))..))).))).(((((((((((((((......))))).....)))))))))).....------.((------..(((((......)))))...)). ( -43.00)
>DroYak_CAF1 12212 90 - 1
GCGUCG------------------UCAGCGCGGCCGUGGGUGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAA------AGC------AUCGGCACAAAGCUGCCGUCAGCA
((..((------------------.((((...((((((((((((((((((......))))).....))))))))))..((.------...------.))))).....)))).))...)). ( -34.40)
>consensus
GCGUCGUCAGCGUCG_________UCAGCGCCGUCGUGGGUGAAAAUGGCCAAAAUGCCAUUCAGCUUUCGCCCAUUUGAA______AGCAUCGUCAUCGACACAAAGCUGCCGUCAGCA
..((((...(((............((((.......(((((((((((((((......))))).....))))))))))))))............)))...)))).....((((....)))). (-27.03 = -27.58 +   0.55) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:28:22 2006